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Difficulty level: Medium 


Computational Reproducibility with the shell, Git and Docker

This workshop provides an overview over tools for computational reproducibility in research. At the end of this workshop participants will be able to navigate via the shell and use it for version control with Git. They will know what types of projects require which forms of computing environments...

Keywords: scientific software, reproducibility, docker container, version control, shell

Resource type: slides

Computational Reproducibility with the shell, Git and Docker https://pan-training.eu/materials/computational-reproducibility-with-the-shell-git-and-docker This workshop provides an overview over tools for computational reproducibility in research. At the end of this workshop participants will be able to navigate via the shell and use it for version control with Git. They will know what types of projects require which forms of computing environments and be able to set up a Docker container to run computations in a reproducible way. scientific software, reproducibility, docker container, version control, shell research data scientist PhD students researchers scientists
Containerized Serial Crystallography “CrystFEL” VISA workflow

Experiments generate up to 150 TB per day of data saved at the measurement facility. Such large datasets are impractical for users to take home. Subsequent analysis needs to be performed remotely making it attractive for deployment as a cloud-like use case. Involving EOSC in the analysis and...

Scientific topics: crystallography

Keywords: CrystFEL, Serial crystallography, pulsed X-ray beam, VISA

Resource type: workflow

Containerized Serial Crystallography “CrystFEL” VISA workflow https://pan-training.eu/materials/containerized-serial-crystallography-crystfel-visa-workflow Experiments generate up to 150 TB per day of data saved at the measurement facility. Such large datasets are impractical for users to take home. Subsequent analysis needs to be performed remotely making it attractive for deployment as a cloud-like use case. Involving EOSC in the analysis and re-use of this data is an appropriate use case. Serial crystallography is a beam-line technique for collecting information on the structure of a protein without growing large protein crystals. Instead, a large number of small protein crystals are held in a pulsed X-ray beam. In a second step, the series of produced images are used to reconstruct a precise 3-D image of the protein structure. Serial crystallography is the preferred technique for obtaining diffraction data of proteins at room temperature, where radiation damage from the X-ray beam starts rapidly. The standard software for analysing serial crystallography is “CrystFEL”. The proposed workflow was rendered in a standard fashion, which would allow it to be easily adopted by arbitrary systems or also other containerized applications. The only requirements are an Apptainer installation on the system and a Docker or Singularity/Apptainer image of the application, as well as an adjustment of the configuration file for the wrapper script. crystallography CrystFEL, Serial crystallography, pulsed X-ray beam, VISA research data scientist scientific
Full-field Tomography at PSI

This workflow has some details on the instrument the data is produced from (TOMCAT beamline) and the infrastructure PSI has concerning their data. If you are more interested in the science and want to reproduce the data and not bother with the surrounding details/context, please refer to the...

Keywords: synchrotron, imaging, Jupyter notebooks, Python, Pulmonary arterial hypertension

Resource type: workflow

Full-field Tomography at PSI https://pan-training.eu/materials/full-field-tomography-at-psi This workflow has some details on the instrument the data is produced from (TOMCAT beamline) and the infrastructure PSI has concerning their data. If you are more interested in the science and want to reproduce the data and not bother with the surrounding details/context, please refer to the Pulmonary arterial hypertension research workflow. Full-field Tomography at PSI Tomography datasets often present large volumes (100 GBs - few TBs) difficult to compress and transfer. The tomographic reconstruction is highly demanding on compute (GPU) and storage resources for the intermediate and/or final result. In addition, the optional image segmentation step may be demanding on computer memory. The offline analysis (after experiment) could be performed remotely by users at home making it attractive for deployment as a cloud-like use case. Finally, this technique is applied at many facilities and in different scientific domains - therefore a portable result is more useful. This entire process is illustrated with a typical experiment. synchrotron, imaging, Jupyter notebooks, Python, Pulmonary arterial hypertension research data scientist life scientists
Training Workflow on Terahertz Spectroscopy at TELBE

The radiation source ELBE (Electron Linac for beams with high Brilliance and low Emittance) at the Helmholtz Centre Dresden Rossendorf (HZDR) can produce several kinds of secondary radiations. THz radiation is one of them and can be used with a typical pulse frequency of 100 kHz as a stimulation...

Scientific topics: spectroscopy, THz photon probe

Keywords: terahertz, Higgs, dataset, data analysis, spectroscopy, FAIR, training, TELBE, photon, metadata, TELBE

Resource type: lesson, workflow, training

Training Workflow on Terahertz Spectroscopy at TELBE https://pan-training.eu/materials/terahertz-spectroscopy-workflow The radiation source ELBE (Electron Linac for beams with high Brilliance and low Emittance) at the Helmholtz Centre Dresden Rossendorf (HZDR) can produce several kinds of secondary radiations. THz radiation is one of them and can be used with a typical pulse frequency of 100 kHz as a stimulation source for elementary low-energy degrees of freedom in matter. In this training workflow brings together background information of the experiment, the facility used, as well as the processing techniques and steps to understand the data generated by the experiment: * The open accessible dataset * The software * Services to execute the analysis spectroscopy THz photon probe terahertz, Higgs, dataset, data analysis, spectroscopy, FAIR, training, TELBE, photon, metadata, TELBE PaN Community beamline users graduate students
ILL's PhD talks

This YouTube playlist displays the ILL PhD seminars, recorded in winter and spring 2021. We thank all the speakers who have agreed to have their presentation shared in this collection, curated by Valerie Duchasténier and Steph Monfront.

Scientific topics: neutron scattering, small angle neutron scattering, time-of-flight spectrometry, magnetism technique, neutron time of flight technique

Keywords: neutron scattering theorie, neutron transport , monochromization, polarized neutrons, multi grid detectors, guide fields and solenoids, quasi-elastic neutron scattering, Small Angle Neutron Scattering, time-of-flight, magnetism and neutrons, ultra cold neutrons, Nuclear Physics

Resource type: video

ILL's PhD talks https://pan-training.eu/materials/ill-s-phd-talks This YouTube playlist displays the ILL PhD seminars, recorded in winter and spring 2021. We thank all the speakers who have agreed to have their presentation shared in this collection, curated by Valerie Duchasténier and Steph Monfront. neutron scattering small angle neutron scattering time-of-flight spectrometry magnetism technique neutron time of flight technique neutron scattering theorie, neutron transport , monochromization, polarized neutrons, multi grid detectors, guide fields and solenoids, quasi-elastic neutron scattering, Small Angle Neutron Scattering, time-of-flight, magnetism and neutrons, ultra cold neutrons, Nuclear Physics PhD students
Offline data analysis tutorial

Tutorial on European XFEL offline data analysis as per example of MID instrument data

Scientific topics: small angle x-ray scattering

Keywords: Extra-data, Extra-geom, pyFAI, data analysis

Resource type: jupyter notebook

Offline data analysis tutorial https://pan-training.eu/materials/offline-analysis-tutorial Tutorial on European XFEL offline data analysis as per example of MID instrument data small angle x-ray scattering Extra-data, Extra-geom, pyFAI, data analysis PaN users beamline users research data scientist
Advanced infrastructure for PIDs in Photon and Neutron RIs

This deliverable accumulates results of ExPaNDS works on the topic of persistent identifiers (PIDs) in facilities research. It refers to the substantial effort of persistent identifiers adoption in facilities and in a larger research ecosystem, and provides a general guidance, as well as...

Keywords: persistent identifiers, wp2-ExPaNDS

Resource type: project deliverable

Advanced infrastructure for PIDs in Photon and Neutron RIs https://pan-training.eu/materials/advanced-infrastructure-for-pids-in-photon-and-neutron-ris This deliverable accumulates results of ExPaNDS works on the topic of persistent identifiers (PIDs) in facilities research. It refers to the substantial effort of persistent identifiers adoption in facilities and in a larger research ecosystem, and provides a general guidance, as well as prioritised recommendations for research information practitioners who consider going beyond the current levels of persistent identifiers adoption by photon and neutron research infrastructures. persistent identifiers, wp2-ExPaNDS facility staff scientists
Introduction to neutron sources

Introduction to Neutron Sources by Dr. Márton Markó from CERIC’s Hungarian Partner Facility, Budapest Neutron Center (BNC)

Keywords: neutron sources

Resource type: video

Introduction to neutron sources https://pan-training.eu/materials/introduction-to-neutron-sources Introduction to Neutron Sources by Dr. Márton Markó from CERIC’s Hungarian Partner Facility, Budapest Neutron Center (BNC) neutron sources PaN Community PaN users PhD students
Introduction to Soft X-ray Transmission and Emission Microscope, TwinMic at Elettra Sincrotrone Trieste

Introduction to the TwinMic Beamline: Soft X-ray Transmission and Emission Microscope at the CERIC Italian partner facility, Elettra Sincrotrone Trieste ---TwinMic beamline webpage in the CERIC website:...

Keywords: soft X-ray Microscopy, synchrotron, Central European Research Infrastructure Consortium, CERIC, synchrotron beamline, microscopy, electrochemistry, battery research, Heritage Science, Elettra synchrotron, Elettra Sincrotrone Trieste, life sciences, microscope

Resource type: video

Introduction to Soft X-ray Transmission and Emission Microscope, TwinMic at Elettra Sincrotrone Trieste https://pan-training.eu/materials/introduction-to-soft-x-ray-transmission-and-emission-microscope-twinmic-at-elettra-sincrotrone-trieste Introduction to the TwinMic Beamline: Soft X-ray Transmission and Emission Microscope at the CERIC Italian partner facility, Elettra Sincrotrone Trieste ---TwinMic beamline webpage in the CERIC website: https://www.ceric-eric.eu/lab-instrument/soft-x-ray-transmission-and-emission-microscope/ ---TwinMic beamline webpage in the Elettra website: https://www.elettra.trieste.it/elettra-beamlines/twinmic.html soft X-ray Microscopy, synchrotron, Central European Research Infrastructure Consortium, CERIC, synchrotron beamline, microscopy, electrochemistry, battery research, Heritage Science, Elettra synchrotron, Elettra Sincrotrone Trieste, life sciences, microscope researchers scientists PhD students chemists physicists biologists
Introduction to High-Resolution Transmission Electron Microscopy (HRTEM) and Electron Paramagnetic Resonance (EPR) at NIMP

Introduction, by Corneliu Ghica and Mariana Stefan, to High-Resolution Transmission Electron Microscopy (HRTEM) and Electron Paramagnetic Resonance (EPR) at the National Institute of Materials Physics in Magurele, Romania HRTEM webpage:...

Keywords: High-Resolution Transmission Electron Microscopy (HRTEM), Electron Paramagnetic Resonance (EPR), CERIC, Central European Research Infrastructure Consortium, National Institute of Materials Physics, life sciences, Materials Science, Heritage Science, astrobiology, biomedical nanomaterials, radiation detection, radiation conversion, semiconductors, insulating materials

Resource type: video

Introduction to High-Resolution Transmission Electron Microscopy (HRTEM) and Electron Paramagnetic Resonance (EPR) at NIMP https://pan-training.eu/materials/introduction-to-high-resolution-transmission-electron-microscopy-hrtem-and-electron-paramagnetic-resonance-epr-at-nimp Introduction, by Corneliu Ghica and Mariana Stefan, to High-Resolution Transmission Electron Microscopy (HRTEM) and Electron Paramagnetic Resonance (EPR) at the National Institute of Materials Physics in Magurele, Romania HRTEM webpage: https://www.ceric-eric.eu/lab-instrument/high-resolution-transmission-electron-microscopy/ EPR webpage: https://www.ceric-eric.eu/lab-instrument/electron-paramagnetic-resonance/ High-Resolution Transmission Electron Microscopy (HRTEM), Electron Paramagnetic Resonance (EPR), CERIC, Central European Research Infrastructure Consortium, National Institute of Materials Physics, life sciences, Materials Science, Heritage Science, astrobiology, biomedical nanomaterials, radiation detection, radiation conversion, semiconductors, insulating materials researchers scientists PhD students physicists material scientists
Introduction to solid-State Nuclear Magnetic Resonance (NMR) at the Slovenian NMR Centre

Introduction to Solid-State Nuclear Magnetic Resonance (NMR) at the CERIC Slovenian partner facility, the Slovenian NMR Centre at the National Institute of Chemistry in Ljubljana by Gregor Mali and Andraž Krajnc Link to related NMR webpages:...

Keywords: Solid-state nuclear magnetic resonance, NMR, life sciences, battery research, pharmaceutical research, NMR spectra, NMR spectroscopy, Slovenian NMR Centre, CERIC, Central European Research Infrastructure Consortium

Resource type: video

Introduction to solid-State Nuclear Magnetic Resonance (NMR) at the Slovenian NMR Centre https://pan-training.eu/materials/introduction-to-solid-state-nuclear-magnetic-resonance-nmr-at-the-slovenian-nmr-centre Introduction to Solid-State Nuclear Magnetic Resonance (NMR) at the CERIC Slovenian partner facility, the Slovenian NMR Centre at the National Institute of Chemistry in Ljubljana by Gregor Mali and Andraž Krajnc Link to related NMR webpages: https://www.ceric-eric.eu/lab-instrument/600-mhz-nuclear-magnetic-resonance-spectometer-2/ Solid-state nuclear magnetic resonance, NMR, life sciences, battery research, pharmaceutical research, NMR spectra, NMR spectroscopy, Slovenian NMR Centre, CERIC, Central European Research Infrastructure Consortium researchers scientists PhD students researchers in energy materials chemists
Introduction to Liquid-State Nuclear Magnetic Resonance (NMR)

Introduction to Liquid-State Nuclear Magnetic Resonance (NMR) at the CERIC Slovenian partner facility, the Slovenian NMR Centre at the National Institute of Chemistry in Ljubljana To get more insights on NMR spectroscopy, watch also the video on Solid-state NMR at: https://youtu.be/RVMAKM6RnRM

Keywords: Liquid-state NMR, NMR, Nuclear Magnetic Resonance, life sciences, COVID research, nucleic acids research, biochemistry, drug development

Resource type: video

Introduction to Liquid-State Nuclear Magnetic Resonance (NMR) https://pan-training.eu/materials/introduction-to-liquid-state-nuclear-magnetic-resonance-nmr Introduction to Liquid-State Nuclear Magnetic Resonance (NMR) at the CERIC Slovenian partner facility, the Slovenian NMR Centre at the National Institute of Chemistry in Ljubljana To get more insights on NMR spectroscopy, watch also the video on Solid-state NMR at: https://youtu.be/RVMAKM6RnRM Liquid-state NMR, NMR, Nuclear Magnetic Resonance, life sciences, COVID research, nucleic acids research, biochemistry, drug development scientists researchers PhD students biochemists chemists
Neutron Diffractometer with a Position Sensitive Detector (PSD) at BNC

Introduction by Margit Fabian, to the Neutron Diffractometer with a Position Sensitive Detector (PSD) at the the CERIC Hungarian partner facility, the Budapest Neutron Centre of the Centre for Energy Research (EK) PSD webpage:...

Keywords: Budapest Neutron Centre, Centre for Energy Research, Neutron Diffractometer with Position Sensitive Detector, neutron research, neutron diffractometry, optical medicine, radioactive waste stabilization, laser development, human bone regeneration, battery research, solid-state batteries, neutron powder diffraction

Resource type: video

Neutron Diffractometer with a Position Sensitive Detector (PSD) at BNC https://pan-training.eu/materials/neutron-diffractometer-with-a-position-sensitive-detector-psd-at-bnc Introduction by Margit Fabian, to the Neutron Diffractometer with a Position Sensitive Detector (PSD) at the the CERIC Hungarian partner facility, the Budapest Neutron Centre of the Centre for Energy Research (EK) PSD webpage: https://www.ceric-eric.eu/lab-instrument/neutron-diffractometer-with-a-position-sensitive-detector-system/ Budapest Neutron Centre, Centre for Energy Research, Neutron Diffractometer with Position Sensitive Detector, neutron research, neutron diffractometry, optical medicine, radioactive waste stabilization, laser development, human bone regeneration, battery research, solid-state batteries, neutron powder diffraction scientists researchers PhD students researchers in energy materials
Introduction to Angle Resolved Photoelectron Spectroscopy - ARPES Beamline at the SOLARIS synchrotron

Introduction to the ARPES Beamline by Prof. Jacek J. Kolodziej and Natalia Olszowska: Angle Resolved Photoelectron Spectroscopy at the CERIC Polish partner facility, the National Synchrotron Radiation Centre SOLARIS in Krakow, Poland ARPES webpage:...

Keywords: photoemission spectroscopy, Angle Resolved Photoemission Spectroscopy, superconducotrs, semiconductors, graphene research, 2D materials, topological insulators

Resource type: video

Introduction to Angle Resolved Photoelectron Spectroscopy - ARPES Beamline at the SOLARIS synchrotron https://pan-training.eu/materials/introduction-to-angle-resolved-photoelectron-spectroscopy-arpes-beamline-at-the-solaris-synchrotron Introduction to the ARPES Beamline by Prof. Jacek J. Kolodziej and Natalia Olszowska: Angle Resolved Photoelectron Spectroscopy at the CERIC Polish partner facility, the National Synchrotron Radiation Centre SOLARIS in Krakow, Poland ARPES webpage: https://www.ceric-eric.eu/lab-instrument/ultra-angle-resolved-photoelectron-spectroscopy/ photoemission spectroscopy, Angle Resolved Photoemission Spectroscopy, superconducotrs, semiconductors, graphene research, 2D materials, topological insulators scientists researchers Materials scientists PhD students
Introduction to Small-Angle X-ray Scattering - SAXS beamline at the TUGraz Outstation at the Elettra synchrotron

Introduction to the SAXS Beamline by Heinz Amenitsch and Barbara Sartori: : Small-Angle X-ray Scattering at the CERIC Austrian partner facility of the Graz University of Technology at the Elettra synchrotron in Trieste, Italy Link to SAXS webpage:...

Keywords: Small-Angle X-ray scattering, Materials Science, COVID research, life sciences, drug delivery, surface science

Resource type: video

Introduction to Small-Angle X-ray Scattering - SAXS beamline at the TUGraz Outstation at the Elettra synchrotron https://pan-training.eu/materials/introduction-to-small-angle-x-ray-scattering-saxs-beamline-at-the-tugraz-outstation-at-the-elettra-synchrotron Introduction to the SAXS Beamline by Heinz Amenitsch and Barbara Sartori: : Small-Angle X-ray Scattering at the CERIC Austrian partner facility of the Graz University of Technology at the Elettra synchrotron in Trieste, Italy Link to SAXS webpage: https://www.ceric-eric.eu/lab-instrument/small-angle-x-ray-scattering/ Small-Angle X-ray scattering, Materials Science, COVID research, life sciences, drug delivery, surface science scientists researchers Materials scientists biologists chemists life scientists
Introduction to SANS: Small Angle Neutron Scattering at BNC

Introduction to SANS Introduction to SANS by Adél Len and László Almásy: Small Angle Neutron Scattering at the CERIC Hungarian partner facility, the Budapest Neutron Centre of the Centre for Energy Research (EK) Link to SANS webpage:...

Keywords: neutron scattering, Small Angle Neutron Scattering, Materials Science, drug delivery, Heritage Science, pharmaceutical research

Resource type: video

Introduction to SANS: Small Angle Neutron Scattering at BNC https://pan-training.eu/materials/introduction-to-sans-small-angle-neutron-scattering-at-bnc Introduction to SANS Introduction to SANS by Adél Len and László Almásy: Small Angle Neutron Scattering at the CERIC Hungarian partner facility, the Budapest Neutron Centre of the Centre for Energy Research (EK) Link to SANS webpage: https://www.ceric-eric.eu/lab-instrument/small-angle-neutron-scattering-diffractometer/ neutron scattering, Small Angle Neutron Scattering, Materials Science, drug delivery, Heritage Science, pharmaceutical research scientists researchers archaeologist biologists Materials scientists
Introduction to PGAA: Prompt-Gamma Neutron Activation Analysis and Neutron Imaging at BNC

Introduction by László Szentmiklósi, to Prompt-Gamma Neutron Activation Analysis (PGAA) and Neutron Imaging at the the CERIC-ERIC Hungarian partner facility, the Budapest Neutron Centre of the Centre for Energy Research (EK) Link to PGAA webpage:...

Keywords: Prompt-Gamma Neutron Activation Analysis, PGAA, Neutron imaging, archaeology, Materials Science, Heritage Science, Engineering

Resource type: video

Introduction to PGAA: Prompt-Gamma Neutron Activation Analysis and Neutron Imaging at BNC https://pan-training.eu/materials/introduction-to-pgaa-prompt-gamma-neutron-activation-analysis-and-neutron-imaging-at-bnc Introduction by László Szentmiklósi, to Prompt-Gamma Neutron Activation Analysis (PGAA) and Neutron Imaging at the the CERIC-ERIC Hungarian partner facility, the Budapest Neutron Centre of the Centre for Energy Research (EK) Link to PGAA webpage: https://www.ceric-eric.eu/lab-instrument/prompt-gamma-neutron-activation-analysis/ Link to RAD webpage: https://www.ceric-eric.eu/lab-instrument/thermal-radiography-station/ Prompt-Gamma Neutron Activation Analysis, PGAA, Neutron imaging, archaeology, Materials Science, Heritage Science, Engineering researchers PhD students scientists archaeologists Materials scientists engineers experts / scientists in heritage sciences
Introduction to DXRL: Deep X-ray Lithography at the Elettra synchrotron in Trieste

Introduction to DXRL by Benedetta Marmiroli: Deep X-ray Lithography at the CERIC Austrian partner facility of the Graz University of Technology at the Elettra synchrotron in Trieste, Italy ---DXRL webpage on the CERIC website:...

Keywords: CERIC, Central European Research Infrastructure Consortium, deep x-ray lithography, DXRL

Resource type: video

Introduction to DXRL: Deep X-ray Lithography at the Elettra synchrotron in Trieste https://pan-training.eu/materials/introduction-to-dxrl-deep-x-ray-lithography-at-the-elettra-synchrotron-in-trieste Introduction to DXRL by Benedetta Marmiroli: Deep X-ray Lithography at the CERIC Austrian partner facility of the Graz University of Technology at the Elettra synchrotron in Trieste, Italy ---DXRL webpage on the CERIC website: https://www.ceric-eric.eu/lab-instrument/dynamic-light-scattering/ ---DXRL webpage on the Elettra website: https://elettra.eu/elettra-beamlines/dxrl.html CERIC, Central European Research Infrastructure Consortium, deep x-ray lithography, DXRL researchers scientists engineers
CrystFEL tutorial

This tutorial covers most of the main steps of using CrystFEL, and is based on processing some freely available LCLS data. The aim of this page is to give an overall idea of how the programs fit together and equip you with the knowledge you need to get started with processing a serial...

Keywords: CrystFEL, data processing, crystallography, structural biology

Resource type: tutorial

CrystFEL tutorial https://pan-training.eu/materials/crystfel-tutorial This tutorial covers most of the main steps of using CrystFEL, and is based on processing some freely available LCLS data. The aim of this page is to give an overall idea of how the programs fit together and equip you with the knowledge you need to get started with processing a serial crystallography data set on your own. CrystFEL, data processing, crystallography, structural biology Photon Community crystallography
Delivering data services to EOSC

Wiki page recording the ExPaNDS training workshop on data services for EOSC (06/04/2021)

Keywords: OAI-PMH, metadata, harvesting, SciCat, ICAT, B2FIND, OpenAIRE, research data, wp3-ExPaNDS

Resource type: wiki

Delivering data services to EOSC https://pan-training.eu/materials/delivering-data-services-to-eosc Wiki page recording the ExPaNDS training workshop on data services for EOSC (06/04/2021) OAI-PMH, metadata, harvesting, SciCat, ICAT, B2FIND, OpenAIRE, research data, wp3-ExPaNDS data curator research data scientist
Python Laser Image Visualization

Tool showing pictures from different cameras (directories) in a grid and a stepwise counter-based scroll functionality. Most of the layout and (future) filter options are defined by command line to allow an easy integration into an workflow based on CWL, OWL (or Knime). In future developments...

Keywords: Python, Laser, Visualization, Cameras, Laser Ion Acceleration, Qt5

Resource type: software, git

Python Laser Image Visualization https://pan-training.eu/materials/python-laser-image-visualization Tool showing pictures from different cameras (directories) in a grid and a stepwise counter-based scroll functionality. Most of the layout and (future) filter options are defined by command line to allow an easy integration into an workflow based on CWL, OWL (or Knime). In future developments most of the parameters can be changed interactive and saved to a json file which can be used to describe the next workflow inputs, so that an interactive workflow development is possible. Python, Laser, Visualization, Cameras, Laser Ion Acceleration, Qt5 PaN Community Photon Community